Interpretive Summary: The temporal sequence of microbial establishment in the pre-ruminant rumen has important ecological and physiological implications to the economical rearing of replacements, development and health of calves, and ultimately, the productive efficiency of the mature animal. In this study, we conducted a metagenomic analysis of the bovine rumen microbiota in pre-ruminant calves of two developmental stages. Our results demonstrated that consistent with the central dogma of rumen development, the microbial population and the production of volatile fatty acids are necessary for rumen development to proceed. Our results provide insight into developing rumen microbiota dynamics and will ultimately facilitate efforts targeting formulation of optimal early-weaning strategies.
Knowledge obtained from this study will undoubtedly lead to undoubtedly facilitate our understanding of host-microbiota mutualism, which should lead to the improvement of animal and human health.

Technical Abstract:
The temporal sequence of microbial establishment in the rumen of the neonatal ruminant has important ecological and pathophysiological implications. In this study, we characterized the rumen microbiota of pre-ruminant calves fed milk replacer using metagenomic tools. In contrast to the relatively stable rumen microbiota present in 42-day-old calves, microbial communities of 14-day-old calves displayed large variation in phylogenetic composition. Sequences from greater than 24 prokaryotic phyla and 22 eukaryotic phyla were identified in microbial communities of pre-ruminant calves. Bacteroidetes was the predominant phylum in the rumen microbiota of 42-day-old calves, representing up to 80% of the total sequences, followed by Proteobacteria and Firmicutes. However, the phylum-level composition of the rumen microbiota of 14-day-old calves was distinctly different from compositions present in both older pre-ruminant calves and post-weaning cattle. A total of 441 prokaryotic genera, including 217 genera that existed in all samples tested, were identified. The functional diversity of the rumen microbiota was reflected by a sum of 8,298 Pfam protein families identified. One of the most salient features of the rumen microbiota of pre-ruminant calves was its instability during early rumen development. Some protein families, including peptidases and glycoside hydrolases, were more abundant in the rumen microbial ecosystem of older pre-ruminant calves. Consistent with the central dogma of rumen development, the microbial population and the production of volatile fatty acids are necessary for development of ruminal papillae to proceed. Our results provide insight into developing rumen microbiota dynamics and will ultimately facilitate efforts targeting formulation of optimal early-weaning strategies.